The first thing that I have done here is modify the alevin-fry workflow to work with spatial libraries with the unfiltered mode in Alevin-fry. To do this I added the barcode lists for visium_v1 and visium_v2 to s3://nextflow-ccdl-data/reference/10X/barcodes. I then added the corresponding filenames for the barcode files to the barcodes map and included the visium_v1 and visium_v2 options in the technology map. This was all that was needed to allow for unfiltered to work and I tested it with the two benchmarking samples and everything ran smoothly.
While modifying the alevin-fry workflow, I noticed that it was still using the ensembl version 103. Because as part of #157, we want to make sure we are comparing libraries that have been mapped with indices created from the same ensembl version, I updated both the alevin-fry and cellranger/spaceranger workflows to use the ensembl 104 as the default index (we don't have a cellranger ensembl 103 index). Because the name of the cellranger index includes ., it will throw an error in spaceranger since the --id option can only include letters, digits, underscores, and dashes. To get around this, I added an index_name parameter that is a shortened version of the index directory that can be used to tag the output folder when used during benchmarking. I also combined all of the individual index parameters into one index_path.
As a result of this PR we can now include Alevin-fry knee, Alevin-fry unfiltered, and Spaceranger all mapped to the same ensembl version in the ST benchmarking notebook as the next steps.
Closes #158 and also partially addresses #157.
The first thing that I have done here is modify the alevin-fry workflow to work with spatial libraries with the unfiltered mode in Alevin-fry. To do this I added the barcode lists for visium_v1 and visium_v2 to
s3://nextflow-ccdl-data/reference/10X/barcodes. I then added the corresponding filenames for the barcode files to the barcodes map and included thevisium_v1andvisium_v2options in the technology map. This was all that was needed to allow for unfiltered to work and I tested it with the two benchmarking samples and everything ran smoothly.While modifying the alevin-fry workflow, I noticed that it was still using the ensembl version 103. Because as part of #157, we want to make sure we are comparing libraries that have been mapped with indices created from the same ensembl version, I updated both the alevin-fry and cellranger/spaceranger workflows to use the ensembl 104 as the default index (we don't have a cellranger ensembl 103 index). Because the name of the cellranger index includes
., it will throw an error in spaceranger since the--idoption can only include letters, digits, underscores, and dashes. To get around this, I added anindex_nameparameter that is a shortened version of the index directory that can be used to tag the output folder when used during benchmarking. I also combined all of the individual index parameters into oneindex_path.As a result of this PR we can now include Alevin-fry knee, Alevin-fry unfiltered, and Spaceranger all mapped to the same ensembl version in the ST benchmarking notebook as the next steps.